hsdM:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

hsdM

Gene Synonym(s)

ECK4339, b4349, JW4312, Hs, hsm, hsp, rm[1]

Product Desc.

host modification; DNA methylase M[2][3];

Component of [[:Category:Complex:EcoKI restriction-modification system|EcoKI restriction-modification system]][3]

DNA methyltransferase M, host modification of foreign DNA[4]

Product Synonyms(s)

DNA methylase M[1], B4349[2][1], Hsp[2][1], Hsm[2][1], HsdM[2][1] , ECK4339, hsm, hsp, JW4312, b4349

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): hsdMS[2], hsdRMS[3]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

hsdM

Mnemonic

Host specificity

Synonyms

ECK4339, b4349, JW4312, Hs, hsm, hsp, rm[1]

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

98.7 minutes 

MG1655: 4581071..4579482
<gbrowseImage> name=NC_000913:4579482..4581071 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4561023..4559434
<gbrowseImage> name=NC_012967:4559434..4561023 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4517966..4519555
<gbrowseImage> name=NC_012759:4517966..4519555 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4587728..4586139
<gbrowseImage> name=NC_007779:4586139..4587728 source=W3110 preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔhsdM (Keio:JW4312)

deletion

deletion

PMID:16738554

Shigen
CGSC11082[5]

ΔhsdM747::kan

PMID:16738554

CGSC:101414


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW4312

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAACAATAACGATCTGGTCGC

Primer 2:CCTTCCTTCACCCCACCAAACGC

12G5

Kohara Phage

Genobase

PMID:3038334

10H12

Kohara Phage

Genobase

PMID:3038334

zjf-920::Tn10

Linked marker

CAG12019 = CGSC7484[5]

est. P1 cotransduction: % [6]
Synonyms:zjh-901::Tn10, zjg-920::Tn10

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[5]

est. P1 cotransduction: 62% [6]
Synonyms:zjj-202::Tn10, zji-202::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10458

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10458

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000451

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948872

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0453

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014260

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

HsdM

Synonyms

DNA methylase M[1], B4349[2][1], Hsp[2][1], Hsm[2][1], HsdM[2][1] , ECK4339, hsm, hsp, JW4312, b4349

Product description

host modification; DNA methylase M[2][3];

Component of [[:Category:Complex:EcoKI restriction-modification system|EcoKI restriction-modification system]][3]

DNA methyltransferase M, host modification of foreign DNA[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0008170

N-methyltransferase activity

PMID:8070417

IMP: Inferred from Mutant Phenotype

F

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002052

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002296

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003356

F

Seeded from EcoCyc (v14.0)

complete

GO:0006306

DNA methylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003356

P

Seeded from EcoCyc (v14.0)

complete

GO:0008168

methyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002052

F

Seeded from EcoCyc (v14.0)

complete

GO:0008168

methyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002296

F

Seeded from EcoCyc (v14.0)

complete

GO:0008168

methyltransferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0489

F

Seeded from EcoCyc (v14.0)

complete

GO:0008170

N-methyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003356

F

Seeded from EcoCyc (v14.0)

complete

GO:0009007

site-specific DNA-methyltransferase (adenine-specific) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.1.1.72

F

Seeded from EcoCyc (v14.0)

complete

GO:0009307

DNA restriction-modification system

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0680

P

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc (v14.0)

complete

GO:0032259

methylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002052

P

Seeded from EcoCyc (v14.0)

complete

GO:0032259

methylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002296

P

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of [[:Category:Complex:EcoKI restriction-modification system|EcoKI restriction-modification system]]

could be indirect

Protein

phoB

PMID:16606699

Experiment(s):EBI-1147889

Protein

nadE

PMID:16606699

Experiment(s):EBI-1147889

Protein

dnaB

PMID:16606699

Experiment(s):EBI-1147889

Protein

gloB

PMID:15690043

Experiment(s):EBI-890115

Protein

ubiD

PMID:15690043

Experiment(s):EBI-890115

Protein

elaB

PMID:15690043

Experiment(s):EBI-895107

Protein

nfi

PMID:15690043

Experiment(s):EBI-895107

Protein

uvrB

PMID:15690043

Experiment(s):EBI-895107

Protein

elaB

PMID:19402753

LCMS(ID Probability):99.6

Protein

nfi

PMID:19402753

LCMS(ID Probability):99.6

Protein

uvrB

PMID:19402753

LCMS(ID Probability):99.6

Protein

gloB

PMID:19402753

MALDI(Z-score):23.733412

Protein

ubiD

PMID:19402753

MALDI(Z-score):27.209154

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MNNNDLVAKL WKLCDNLRDG GVSYQNYVNE LASLLFLKMC KETGQEAEYL PEGYRWDDLK
SRIGQEQLQF YRKMLVHLGE DDKKLVQAVF HNVSTTITEP KQITALVSNM DSLDWYNGAH
GKSRDDFGDM YEGLLQKNAN ETKSGAGQYF TPRPLIKTII HLLKPQPREV VQDPAAGTAG
FLIEADRYVK SQTNDLDDLD GDTQDFQIHR AFIGLELVPG TRRLALMNCL LHDIEGNLDH
GGAIRLGNTL GSDGENLPKA HIVATNPPFG SAAGTNITRT FVHPTSNKQL CFMQHIIETL
HPGGRAAVVV PDNVLFEGGK GTDIRRDLMD KCHLHTILRL PTGIFYAQGV KTNVLFFTKG
TVANPNQDKN CTDDVWVYDL RTNMPSFGKR TPFTDEHLQP FERVYGEDPH GLSPRTEGEW
SFNAEETEVA DSEENKNTDQ HLATSRWRKF SREWIRTAKS DSLDISWLKD KDSIDADSLP
EPDVLAAEAM GELVQALSEL DALMRELGAS DEADLQRQLL EEAFGGVKE
Length

529

Mol. Wt

59.307 kDa

pI

5.0 (calculated)

Extinction coefficient

61,880 - 62,630 (calc based on 12 Y, 8 W, and 6 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

122..450

PF02384 N-6 DNA Methylase

PMID:19920124

Domain

6..110

PF12161 HsdM N-terminal domain

PMID:19920124

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=hsdM taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16132170

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948872

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014260

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P08957

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10458

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10458

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948872

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000451

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0453

Escherichia coli str. K-12 substr. MG1655

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Notes

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

3.48E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

13.165+/-0.084

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.024229075

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

2090

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

450

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

1135

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

hsdMS

hsdRMS

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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:4581051..4581091 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b4349 (EcoliWiki Page)

NCBI GEO profiles for hsdM

microarray

GenExpDB:b4349 (EcoliWiki Page)

Summary of data for hsdM from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (4580518..4580823) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ09; Well:H2[7]

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Notes

Accessions Related to hsdM Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10458

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0453

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4349

EcoGene

EcoGene:EG10458

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000451

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014260

Escherichia coli str. K-12 substr. MG1655

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Notes

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Apis mellifera

  • ENSAPMP00000024224 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

E. coli O157

Z5947

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

Pfam (EcoliWiki Page)

PF02384 N-6 DNA Methylase

Superfamily (EcoliWiki Page)

SUPERFAMILY:53335

Pfam (EcoliWiki Page)

PF12161 HsdM N-terminal domain

EcoCyc

EcoCyc:EG10458

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10458

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000451

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0453

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014260

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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